Adebayor was among the scorers as big-spending City made a compelling case for their ability to break the stranglehold of the "big four" in England, securing their fourth win out of four.
But he later made apologies over two controversial incidents that marked the game.
The results take Chelsea to 15 points with Manchester United, Manchester City and Spurs all on 12.
EASTLANDS DRAMA
Adebayor, City's 25 million pounds summer signing from Arsenal, headed the third and Shaun Wright-Phillips then finished off a great breakaway.
Adebayor's decision to run the length of the pitch to celebrate his goal in front of the Arsenal fans earned him a booking but the Togo international, who has now scored in all four of City's league games, was quick to apologise.
"I shouldn't have done what I did but the emotion took over me and I'm sorry for what I've done," he told Sky Sports.
After the match had finished, Van Persie issued a statement via the club's official website accusing Adebayor of maliciously stamping on him. The City striker firmly denied that suggestion but expressed sorrow, saying he was trying to kick the ball, not his opponent's head.
"I did not have time to take back my feet," he said. "Because I was trying to kick the ball my feet touched his head. At the end of the game I told him I'm very sorry."
Czech midfielder Tomas Rosicky got Arsenal's late second.
Any thoughts of another upset win soon disappeared, though, as Ryan Giggs equalised with a free kick and Anderson's first goal for the club had the visitors deservedly ahead at half-time.
